I first have to say that you should really scroll through EVERY FOLDER of Guert's mod, you'll get a LOT wiser.
1. Every map has it's own XML file that says what picture it has to take from the map of the shape, like bear said, white is where you swim in, black is where you can't swim in, it ALSO picks the tile set in that same file.The numbers in the tile set stands for the ID they use, to replace tiles with other tiles. Like you have a rock0001 as 1 and replace it with shadow0002 or something, they get switched. Every ID is saved in the XML file that contains the whole map.
2. Bear answered this, even though the size of the map has to use these values: 128, 256, 512, 1024, 2048, 4096... etc, I think, don't know if there's limit. Example: 1024x256 for a very tall map, or 512x2048 for a very wide map.
3. Once again, also the MUSIC is sorted in the XML file, and the background has it's own layers.